CI: Optimized GH actions workflow YAML

Avoids unnecessary jobs in open PRs, removes flake8 in favor of ruff.
Also adds minor style changes for ruff compliance.

.github/workflows/lint_test_coverage.yml

@@ -1,14 +1,11 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Test Coverage Lint
+name: TestCov Lint
 
 on:
   push:
-    branches-ignore:
+    branches:
       - main
+      - release-*
   pull_request:
-    branches: [ "main", "$default_branch" ]
 
 jobs:
   build:
@@ -25,16 +22,16 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install poetry and the package dependencies
+    - name: Dependency installation
+      if: github.event_name == 'pull_request' || github.event_name == 'push'
       run: |
         python -m pip install --upgrade pip
-        python -m pip install poetry nox nox-poetry   
-    - name: Nox TEST session
-      run: |
-        nox -s test
-    - name: Nox COVERAGE session
+        python -m pip install poetry nox nox-poetry
+    - name: TestCoverage
+      if: github.event_name == 'pull_request' || github.event_name == 'push'
       run: |
         nox -s coverage
-    - name: Nox LINTING session
+    - name: Linting
+      if: github.event_name == 'pull_request' || github.event_name == 'push'
       run: |
-        nox -s lint
+        nox -s lint

.gitignore

@@ -166,7 +166,7 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-# Apple 
+# Apple
 .DS_store
 
 # VSCode

NOTICE

@@ -1,4 +1,4 @@
 ageml
 Copyright 2023 The ageml Developers
 
-This product includes software developed at the Computational Neuroimaging Laboratory of the Biobizkaia Health Research Institute, Barakaldo, Basque Country.
+This product includes software developed at the Computational Neuroimaging Laboratory of the Biobizkaia Health Research Institute, Barakaldo, Basque Country.

bin/scripts/debug_classify.py

@@ -1,4 +1,4 @@
 import ageml.commands as commands
 
-if __name__ == '__main__':
-    commands.clinical_classify()
+if __name__ == "__main__":
+    commands.clinical_classify()

bin/scripts/debug_clinical.py

@@ -1,4 +1,4 @@
 import ageml.commands as commands
 
-if __name__ == '__main__':
-    commands.clinical_groups()
+if __name__ == "__main__":
+    commands.clinical_groups()

bin/scripts/debug_factors.py

@@ -1,4 +1,4 @@
 import ageml.commands as commands
 
-if __name__ == '__main__':
-    commands.factor_correlation()
+if __name__ == "__main__":
+    commands.factor_correlation()

bin/scripts/debug_model_age.py

@@ -1,4 +1,4 @@
 import ageml.commands as commands
 
-if __name__ == '__main__':
-    commands.ModelAge()
+if __name__ == "__main__":
+    commands.ModelAge()

docs/CONTRIBUTING.md

@@ -27,15 +27,15 @@ ageml
 │   ├──CONTRIBUTING.md              # Contribution Guidelines.
 │   └──...
 │
-├── resources                       # Folder with figures and other supporting files 
+├── resources                       # Folder with figures and other supporting files
 │
 │
 ├── src                             # Contains all the source code of the package
-│    └── ageml                    
-│         ├── ...   
+│    └── ageml
+│         ├── ...
 │         ├── my_awesome_subpkg1
 │         │   ├── __init__.py
-│         │   └── awesome_fun.py                           
+│         │   └── awesome_fun.py
 │         └── my_awesome_subpkg2
 │             ├── __init__.py
 │             └── awesome_fun.py
@@ -49,8 +49,8 @@ ageml
 │       └── test_awesome_fun
 │
 │
-├── .coverage                       # File to measure code coverage, percentage of tested code lines 
-├── README.md                        
+├── .coverage                       # File to measure code coverage, percentage of tested code lines
+├── README.md
 ├── pyproject.toml                  # Requirements for environment settings, packaging and so on
 ├── poetry.lock                     # Dependency for building the system
 ├── noxfile.py                      # Defines the linting, coverage, pytest sessions

noxfile.py

@@ -22,6 +22,6 @@ def coverage(s: Session) -> None:
 
 @session(reuse_venv=True)
 def lint(s: Session) -> None:
-    # Run pyproject-flake8 entrypoint to support reading configuration from pyproject.toml.
+    # Run the ruff linter, way faster than flake8
     s.run("poetry", "install", external=True)
-    s.run("flake8")
+    s.run("ruff", "check")

pyproject.toml

@@ -30,13 +30,16 @@ scipy = ">=1.10"
 statsmodels = "0.14.0"
 matplotlib = "3.5"
 scikit-learn = "1.3"
-coverage-conditional-plugin = "^0.7.0"
 xgboost = "^2.0.3"
 pillow = "^10.3.0"
 hpsklearn = {git = "https://github.com/hyperopt/hyperopt-sklearn", rev = "4bc286479677a0bfd2178dac4546ea268b3f3b77"}
 
 [tool.poetry.dev-dependencies]
+# Testing and linting tool
 nox-poetry = "*"
+coverage-conditional-plugin = "^0.7.0"
+# Pre-commit
+pre-commit = "^3.0.0"
 # Testing
 pytest = "*"
 pytest-cov = "*"

setup.cfg

@@ -1,19 +1,19 @@
 [flake8]
-exclude = .nox, .pytest_cache, dist, .venv, resources, data, bin, .history, 
+exclude = .nox, .pytest_cache, dist, .venv, resources, data, bin, .history,
 max-line-length = 140
 statistics = True
 # Which LINTING rules to ignore
 ignore = F401, # Imported but unused
         F403, # Unable to detect undefined names
         B028, # No explicit stacklevel keyword argument found
         W293, # blank line contains whitespace (I don't like this rule, interferes with good function indentation)
-        C419, # Unnecessary list comprehension passed to all() prevents short-circuiting - rewrite as a generator 
+        C419, # Unnecessary list comprehension passed to all() prevents short-circuiting - rewrite as a generator
         E702, # Multiple statements on one line (semicolon)
         B023, # Function definition does not bind loop variable 'some_var_name'.
 
-per-file-ignores = 
+per-file-ignores =
         # It poses no inconvenient to violate B006 in this file.
-        tests/test_ageml/test_modelling.py: B006 
+        tests/test_ageml/test_modelling.py: B006
 
 
 [coverage:run]
@@ -25,4 +25,4 @@ plugins =
 [coverage:coverage_conditional_plugin]
 rules =
   "is_installed('django')": has-django
-  "not is_installed('django')": has-no-django
+  "not is_installed('django')": has-no-django

src/ageml/__main__.py

@@ -7,5 +7,5 @@ def main():
     ageml.ui.CLI()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()